THEORY OF DNA-SEQUENCING USING FREE-SOLUTION ELECTROPHORESIS OF PROTEIN-DNA COMPLEXES

Large-scale sequencing projects, like the human genome project, require the development of new DNA separation methods that are more efficient than currently used gel electrophoresis methods. Here, we present the theoretical limits of the free-solution electrophoretic separation of DNA molecules end-labeled with a protein (or another monodisperse chemical) to generate additional friction. We call this new method ELFSE for end-labeled free-solution electrophoresis. Our results are based on a free-draining coil model and the Einstein relation between friction and diffusion. We show that off-the-shelf streptavidin-DNA free solution capillary electrophoresis could already outperform current DNA separation technologies. By using Small loading widths and large monodisperse labeling proteins or chemicals, ELFSE should allow one to resolve over 2000 bases per sequencing reaction within minutes. Therefore, since a sieving network is not necessary, ELFSE might open the way to automated supersequencing systems and dramatically speed up the human genome project.